title: The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron-exon recognition.
abstract: The essential cis- and trans-acting elements required for RNA splicing have been defined, however, the detailed molecular mechanisms underlying intron-exon recognition are still unclear. Here we demonstrate that the ratio between stability of mRNA/DNA and DNA/DNA duplexes near 3'-spice sites is a characteristic feature that can contribute to intron-exon differentiation. Remarkably, throughout all transcripts, the most unstable mRNA/DNA duplexes, compared with the corresponding DNA/DNA duplexes, are situated upstream of the 3'-splice sites and include the polypyrimidine tracts. This characteristic instability is less pronounced in weak alternative splice sites and disease-associated cryptic 3'-splice sites. Our results suggest that this thermodynamic pattern can prevent the re-annealing of mRNA to the DNA template behind the RNA polymerase to ensure access of the splicing machinery to the polypyrimidine tract and the branch point. In support of this mechanism, we demonstrate that RNA/DNA duplex formation at this region prevents pre-spliceosome A complex assembly.
authors.affiliation: Institute of Molecular Biology Roumen Tsanev, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
authors.forename: Marina N
authors.initials: MN
authors.lastname: Nedelcheva-Veleva
authors.forename: Mihail
authors.initials: M
authors.lastname: Sarov
authors.forename: Ivan
authors.initials: I
authors.lastname: Yanakiev
authors.forename: Eva
authors.initials: E
authors.lastname: Mihailovska
authors.forename: Miroslav P
authors.initials: MP
authors.lastname: Ivanov
authors.forename: Greta C
authors.initials: GC
authors.lastname: Panova
authors.forename: Stoyno S
authors.initials: SS
authors.lastname: Stoynov
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D004247:DNA / Q000378:metabolism; D056890:Eukaryota / Q000235:genetics*; D005091:Exons / Q000235:genetics*; D049751:Genome, Helminth / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000378:metabolism; D009711:Nucleotides / Q000235:genetics; D022821:RNA Splice Sites; D020871:RNA Stability / Q000235:genetics; D017381:Spliceosomes / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D009711:Nucleotides; D022821:RNA Splice Sites; D004247:DNA